Hi Roland, thank you very much for your answer, I made it using hdf5_slicer. I'm puzzled though, because in my Python script I copied each dataset into a separate file, so I was expecting nioprocs = 160 to be correct (there are 160 files). Anyway, hdf5_slicer worked perfectly.
Thank you again, Lorenzo Il giorno lun 27 giu 2022 alle ore 15:20 Roland Haas <[email protected]> ha scritto: > Hello Lorenzo, > > There's a metadata nioprocs or so that is rhe number of files. If you > copied all datasets into a single file you must set it to 1. You can use a > tiny Python script to do so, or (I think) hdf5_slicer --out3d_box, or (I > think) hdf5_merge with its --ioprocs option. > > In fact you can use hdf5_slicer to do the extraction for you. There's some > details about this in the response to an earlier question by Maria about > merging files I think. > > Yours, > Roland > > ----- Original Message ----- > From: Lorenzo Ennoggi <[email protected]> > Sent: 2022-06-27 - 07:01 > To: Einstein Toolkit Users <[email protected]> > Subject: [Users] Extracting the last iteration from 3D CarpetIOHDF5 output > files > > > Hello, > > I have a set of 3D output files from CarpetIOHDF5 (rho.xyz_file<n>.h5), > > each containing many iterations, and I want to create a set of new > > CarpetIOHDF5 files containing the data related to the last iteration. I > > have tried something, but I couldn't get anything to work, so I am asking > > for help here. > > > > For each file rho.xyz_file<n>.h5, I used the hdf5_extract utility to > create > > a new file containing the dataset related to the last iteration > > ("HYDROBASE::rho > > it=1067600 tl=0 rl=0 c=<n>") and the group "Parameters and Global > > Attributes". However, when I try to open the set of new files with VisIt > I > > get the following error: > > > > VisIt could not read from the file > >> > "/home/lorenzo/CBD_prod_WZ9_400_140_280_output-0014/Output/rho.xyz_it1067600_tl0_rl0_c* > >> database". > > > > > > The generated error message was: > > > > > > There was an error opening > >> > /home/lorenzo/CBD_prod_WZ9_400_140_280_output-0014/Output/rho.xyz_it1067600_tl0_rl0_c* > >> database. It may be an invalid file. VisIt tried using the following > file > >> format readers to open the file: CarpetHDF5 > > > > > > The following error(s) may be helpful in identifying the problem: > >> *Tried to access an invalid index 1 (Maximum = 0).* > > > > > > I thought that maybe some metadata in the new files are telling VisIt > that > > there are multiple iterations available, which is not true; I'm not > > completely sure this is really the issue, though. > > > > In the new files, the attributes "GH$iteration" and "carpet_global_time" > > from the group "Parameters and Global Attributes" are still respectively > > set to the first iteration (992800) and the first time (148920) available > > in the original files, while I am extracting the last iteration (1067600, > > time 160140). Also, in the new files, the dataset "Grid Structure v5" (a > > string) still contains > > "grid_times:[[[148920,148919.85000000001,148919.69999999998]]]", which > also > > looks wrong. Therefore, I used h5py to generate new files in which I > fixed > > "GH$iteration", "carpet_global_time" and "Grid Structure v5", but I still > > get the same error from VisIt. > > > > I have also thought about re-running the simulation that produced the > > original files from the last checkpoint and just dump the last iteration, > > but that simulation was run some time ago and the code I am using has > > evolved quite a bit in the meantime, to the point that some parameters > are > > not even defined anymore. > > > > Is there any other attribute/dataset I should edit in order to fix the > new > > files? Are there smarter ways to extract an iteration from a set of 3D > > CarpetHDF5 output files? Please let me know if you need additional > > information from my end. > > > > Thank you very much, > > Lorenzo Ennoggi > > _______________________________________________ > > Users mailing list > > [email protected] > > > https://urldefense.com/v3/__http://lists.einsteintoolkit.org/mailman/listinfo/users__;!!DZ3fjg!8ek7C4tvxIysQIy8c3UhecmG8i6HaqZW_HTD-WMedhlEHkX7_FBP7ORbQoGjMqNr2SXd2ekz8pJr7kHksP2S8ShBJg$ > > >
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